Samsung is accused of giving donations to several non-profit foundations operated by Choi Soon-sil, a close friend to President Park Geun-hye.
The donations were allegedly made in exchange for political support of a controversial merger.
The Choi Soon-sil scandal has led to President Park Geun-hye being impeached by South Korea’s parliament last month.
Lee Jae-yong told reporters upon arriving on January 12: “I deeply apologize to the people for failing to show a positive image because of this incident.”
Earlier this week two other Samsung executives were questioned by the special prosecutors, but were treated as witnesses rather than suspects.
The claims against Samsung circle around a merger between the electronics giant’s construction arm, Samsung C&T, and an affiliate company, Cheil Industries.
Prosecutors allege that Samsung gave €2.8 million euros ($3.1 million) to a company co-owned by Choi Soon-sil and her daughter, in return for Park Geun-hye’s support for the deal.
Lee Jae-yong, known professionally as Jay Y. Lee, has already given evidence to politicians over the scandal, but this is the first time he has been questioned as a suspect by investigators.
At the parliamentary hearing in December, Samsung admitted giving a total of 20.4 billion won ($17.46 million) to the two foundations, but denied seeking favors.
Jay Y. Lee also confirmed Samsung gave a horse and money to help the equestrian career of Choi Soon-sil’s daughter, Chung Yoo-ra, something he said he now regretted.
Choi Soon-sil is on trial for charges including corruption and coercion.
President Park Geun-hye’s position began to unravel in October 2016, when details of her friendship with Choi Soon-sil began to emerge.
They included revelations that Park Geun-hye had allowed Choi Soon-sil – who holds no government role – to edit political speeches.
Since then, hundreds of thousands of protestors have gathered every weekend in Seoul to demand Park Geun-hye’s resignation.
Park Geun-hye denies wrongdoing but has apologized for the way she managed her relationship with Choi Soon-sil, who also denies committing criminal offences.
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